M. Chikina

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

This study investigates whether evolutionary rate covariation (ERC) signals reflect physical interactions or other factors, finding weak evidence for physical coevolution and suggesting selective pressures may drive the signal.

Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements

This paper introduces phyloConverge, a method to analyze local convergence in regulatory elements, showing it identifies rate-accelerated CNEs linked to ocular tissues in subterranean mammals.

A cautionary tale on proper use of branch-site models to detect convergent positive selection

The paper warns against misinterpreting branch-site models in comparative genomics, showing how failing to distinguish phylogeny-wide from branch-specific positive selection leads to false inferences and proposes a 'drop-out' test to address this issue.

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter.

The paper uses evolutionary rate covariation to predict the mitochondrial localization of SLC30A9, which is confirmed experimentally as a zinc exporter.

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

The paper identifies coding and noncoding sequences that evolve differently in hairless mammals, revealing distinct evolutionary patterns between protein-coding genes and regulatory elements.

Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context

This paper introduces phylogenetic permulations to calculate accurate p-values for phylogenetic analyses, improving statistical confidence in phenotype-genetic element associations.

Cancer control is a key functionality underlying evolution of extended lifespan in mammals

The paper uses comparative genomics to link evolutionary constraint on cancer-related pathways with extended lifespan in mammals, supporting the role of cancer control in longevity.

Robust methods for detecting convergent shifts in evolutionary rates

The paper improves a method for detecting convergent evolutionary rate shifts by addressing statistical limitations through data transformation and weighted regression.

RERconverge: an R package for associating evolutionary rates with convergent traits

RERconverge associates evolutionary rates with convergent traits across phylogenies, supporting binary and continuous traits with visualization and enrichment tools.